2.1 Main figures
Alpha/Beta Diversities
Huang Lin\(^1\)
\(^1\)NICHD, 6710B Rockledge Drive, Bethesda, MD 20892
September 27, 2021
2. Alpha diversity: Shannon’s diversity index
For the adult population.
P-value is obtained by Wilcoxon Rank Sum Test for alpha diversities.
2.2 Supplementary figures
3. Beta diversity: Bray-Curtis dissimilarity
For the adult population.
P-values are obtained by Permutational Multivariate Analysis of Variance (PERMANOVA) and Permutational Analysis of Multivariate Dispersion (PERMDISP) for beta diversities.
3.1 Main figures
quartz_off_screen
2 quartz_off_screen
2 3.2 Supplementary figures
Session information
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggpubr_0.4.0 qwraps2_0.5.2 magrittr_2.0.1 compositions_2.0-2
[5] vegan_2.5-7 lattice_0.20-44 permute_0.9-5 microbiome_1.14.0
[9] phyloseq_1.36.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[13] purrr_0.3.4 tidyr_1.1.3 tibble_3.1.4 ggplot2_3.3.5
[17] tidyverse_1.3.1 openxlsx_4.2.4 readr_2.0.1
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-2 ggsignif_0.6.3
[4] rio_0.5.27 ellipsis_0.3.2 XVector_0.32.0
[7] fs_1.5.0 rstudioapi_0.13 farver_2.1.0
[10] bit64_4.0.5 fansi_0.5.0 lubridate_1.7.10
[13] xml2_1.3.2 codetools_0.2-18 splines_4.1.1
[16] robustbase_0.93-8 knitr_1.34 ade4_1.7-18
[19] jsonlite_1.7.2 broom_0.7.9 cluster_2.1.2
[22] dbplyr_2.1.1 compiler_4.1.1 httr_1.4.2
[25] backports_1.2.1 assertthat_0.2.1 Matrix_1.3-4
[28] fastmap_1.1.0 cli_3.0.1 htmltools_0.5.2
[31] tools_4.1.1 igraph_1.2.6 gtable_0.3.0
[34] glue_1.4.2 GenomeInfoDbData_1.2.6 reshape2_1.4.4
[37] Rcpp_1.0.7 carData_3.0-4 Biobase_2.52.0
[40] cellranger_1.1.0 jquerylib_0.1.4 vctrs_0.3.8
[43] Biostrings_2.60.2 rhdf5filters_1.4.0 multtest_2.48.0
[46] ape_5.5 nlme_3.1-153 iterators_1.0.13
[49] tensorA_0.36.2 xfun_0.26 rvest_1.0.1
[52] lifecycle_1.0.0 rstatix_0.7.0 DEoptimR_1.0-9
[55] zlibbioc_1.38.0 MASS_7.3-54 scales_1.1.1
[58] vroom_1.5.5 hms_1.1.0 parallel_4.1.1
[61] biomformat_1.20.0 rhdf5_2.36.0 RColorBrewer_1.1-2
[64] curl_4.3.2 yaml_2.2.1 gridExtra_2.3
[67] stringi_1.7.4 highr_0.9 S4Vectors_0.30.0
[70] foreach_1.5.1 BiocGenerics_0.38.0 zip_2.2.0
[73] GenomeInfoDb_1.28.4 rlang_0.4.11 pkgconfig_2.0.3
[76] bitops_1.0-7 evaluate_0.14 Rhdf5lib_1.14.2
[79] labeling_0.4.2 cowplot_1.1.1 bit_4.0.4
[82] tidyselect_1.1.1 plyr_1.8.6 R6_2.5.1
[85] IRanges_2.26.0 generics_0.1.0 DBI_1.1.1
[88] foreign_0.8-81 pillar_1.6.2 haven_2.4.3
[91] withr_2.4.2 mgcv_1.8-36 abind_1.4-5
[94] survival_3.2-13 RCurl_1.98-1.5 bayesm_3.1-4
[97] car_3.0-11 modelr_0.1.8 crayon_1.4.1
[100] utf8_1.2.2 tzdb_0.1.2 rmarkdown_2.11
[103] grid_4.1.1 readxl_1.3.1 data.table_1.14.0
[106] reprex_2.0.1 digest_0.6.27 stats4_4.1.1
[109] munsell_0.5.0